ADF Modeling Suite --
developed and distributed by
Software for
Chemistry & Materials (SCM) https://www.scm.com.
Based around Amsterdam Density Functional, the ADF Modeling Suite has
molecular & periodic DFT, semi-empirical, reactive MD, and fluid
thermodynamic capabilities with an integrated GUI. It is used by
researchers for many different applications in chemistry, materials
science and chemical engineering.

ADME DB -- ADME DB is a database containing
the latest and most comprehensive data on interactions of substances
with Drug Metabolizing Enzymes and Drug Transporters. It is designed for
use in drug research and development, including
drug-drug interactions and ADME (Absorption, Distribution, Metabolism
and Excretion) studies. The information is organized by category
(therapeutic area), drug name, enzyme, reaction, and type. ADME DB is
supported by chemical/metabolite structures as well
as kinetic values found in the literature. The database is available
online and completely searchable by keywords or chemical structures.
Advanced searches are also available to support investigational studies
on drug-drug interactions.http://www.fqs.pl/chemistry_materials_life_science/products/adme_db

ADMEWORKS ModelBuilder --
ADMEWORKS ModelBuilder is a tool
dedicated for building QSAR/QSPR models that can later be used for
predicting various chemical and biological properties of compounds. A
set of data on molecular structures and their respective
experimental values of the property of interest is a prerequisite for
every model building. Two classes of models (Qualitative and
Quantitative) can be built using various algorithms.
http://www.fqs.pl/chemistry_materials_life_science/products/ddi_simulator

ADMEWORKS Predictor --
ADMEWORKS Predictor is a
high-speed virtual (in silico) screening system intended for
simultaneous evaluation of the ADMET properties of compounds. It
complements existing In Silico technologies for evaluating
pharmacological
properties. Simultaneous evaluation of the pharmacological as well as
the ADMET properties of compounds is useful in the discovery phase to
produce balanced quality hits, and also in the lead optimization phase
to lessen the occurrence of faulty leads.
http://www.fqs.pl/chemistry_materials_life_science/products/admeworks_predictor

Aggrescan3D - web server for prediction of aggregation propensity in
protein structures and rational design of protein solubility. It is freely
available to all users at http://biocomp.chem.uw.edu.pl/A3D and there is no
login requirement. In dynamic mode, A3D takes into account the flexibility
of natural and designed proteins.

PoseViewhttp://www.biosolveit.de/PoseView/
is a software tools to generate 2D-images (png, svg and pdf)
of 3D Protein-Ligand
complexes. Note that PoseView images are available for the majority of
PDB-structures on the PDB web site.

HYDEhttp://www.biosolveit.de/Hyde/
in an entirely new approach to assessing binding affinities.
Hyde is entirely based
on physics-principles and has not been trained or calibrated on
experimental data.
Hyde provides visual feedback at atomic detail.

ReCorehttp://www.biosolveit.de/ReCore/
instantaneously generates scaffold replacement ideas with the objective,
to leave
the 'old' side chains in place. It is also applicable in fragment-merging,
fragment-linking and fragment-growing scenarios.

CABS-dock - web server for protein-peptide docking. It is freely available
to all users at http://biocomp.chem.uw.edu.pl/CABSdock and there is no
login requirement. CABS-dock performs simulation search for the binding
site allowing for full flexibility of the peptide and small fluctuations of
the receptor backbone in the default mode. In the advanced mode, CABS-dock
also enables large-scale flexibility of protein receptor structure.
CABS-dock animation movies are available at
https://www.youtube.com/user/sek177

CABS-flex - web server for fast simulations of protein structure
fluctuations. It is freely available to all users at
http://biocomp.chem.uw.edu.pl/CABSflex and there is no login requirement.
CABS-flex was shown to be an efficient alternative to classical all-atom
molecular dynamics. Also, it has been shown, that relative fluctuations of
protein residues obtained from CABS-flex are well correlated to those of
NMR ensembles. CABS-flex animation movies are available at
https://www.youtube.com/user/sek177

CABS-fold - web server for protein structure prediction from sequence only (de novo modeling) and also using alternative templates (consensus modeling).
It is freely available to all users at
http://biocomp.chem.uw.edu.pl/CABSfold and there is no login requirement.
Except for template data, fragmentary distance restraints can also be
incorporated into the modeling process.

CambridgeSoft Software --
CambridgeSoft Corporation is a
leading supplier of discovery, collaboration, and knowledge enterprise
solutions, desktop software, scientific databases and consulting
services to the pharmaceutical, biotechnology, and
chemical industries. The Company provides enterprise solutions, desktop
software, scientific databases, and professional services for
biotechnology, drug discovery and chemical research, including software,
databases, and web sites which enable customers to
create, analyze and communicate chemical, biological, and scientific
information more effectively.
http://www.fqs.pl/chemistry_materials_life_science/products/cambridgesoft_software

Cell Illustrator --
Cell Illustrator is a powerful
tool that enables biologists to draw, model, elucidate and simulate
complex biological processes and systems. It has outstanding drawing
capabilities, moreover it allows researchers to model
metabolic pathways, signal transduction cascades, gene regulatory
networks as well as dynamic interactions of various biological entities
such as genomic DNA, mRNA and proteins.
http://www.fqs.pl/chemistry_materials_life_science/products/cell_illustrator

Chimera -- package for molecular modeling: atom-type
identification, association of structures with sequence alignments,
and interactive contouring of volume data (for example, electron density
or electrostatic potential). Results from several molecular dynamics
programs and from DOCK can be viewed and analyzed. Free for academia. --
http://www.cgl.ucsf.edu/chimera/

CLIFF -- is a powerful program which provides a series of functionality, which goes beyond a simple conversion tool: -- http://www.mol-net.de/

CMDBioscience, LLC -- CMD bioscience
( http://www.cmdbioscience.com/ )
specializes in the use of novel proprietary computational methods to model
and engineer clinically important protein-protein and protein-peptide
interactions. Our Affinity algorithm is designed to predict
protein-protein / protein-peptide binding affinities; it is fast enough for
use as a scoring function and will be made freely available to the academic
community. Other key, proprietary computational tools employed by scientists
at CMD Bioscience include Ensemble and Transcend. These
groundbreaking search algorithms, when interfaced with Affinity,
allow CMD scientists to efficiently design novel peptides and proteins

HYPERCUBE. INC. -- http://www.hyper.com/ HyperChem package:
Computational methods include molecular mechanics, molecular dynamics,
and semi-empirical and ab-initio molecular orbital methods,
as well as density functional theory. HyperChem is applicable
to macromolecules as well as small molecules and is scriptable.

Molexel-- an interactive molecular graphics program to visualize molecular and
electronic structure data from a number of electronic structure program outputs
(Gaussian, Gamess, ADF...) as well as from XYZ and PDB files -- http://www.cscs.ch/molekel/

MolSoft -- http://www.molsoft.com/: Molsoft is a La Jolla, California based company that is a primary source of new breakthrough technologies in: molecular graphics and visualization, molecular modeling, docking and virtual screening, computational biology and cheminformatics.

ICM-Browser Molecule Visualization

ICM-Browser (Free Download) -- Software for browsing
molecules and making fully-interactive slides for embedding in PowerPoint
and the Web using ActiveiCM.

ICM-Browser-Pro -- A high quality visualizer and annotator
for three dimensional molecular structures, sequences and alignments,
chemical spreadsheets and biological data.

SageMD -- Visualizer/builder for crystal structures
and interfaces. Classical MM/MD. Support for popular file formats
for export/import. Extensve database of inorganic structures.
Free for academia and inexpensive for industrial researchers.
http://sagemd.com

SCIGRESS --
SCIGRESS is a unique desktop
molecular modeling software package that can apply a wide range of
computational models to all types of molecular systems, from small
organic molecules, to inorganics, polymers, materials
systems and whole proteins. SCIGRESS speeds time-to-discovery by
providing powerful computing and analytical tools designed for
experimental scientists.
http://www.fqs.pl/chemistry_materials_life_science/products/scigress

SKIN-CAD --
SKIN-CAD is a general simulation
software for the skin and body pharmacokinetics following transdermal
and topical drug delivery. SKIN-CAD predicts dynamic profiles of skin
permeation and distribution and blood concentration
under various modes of transdermal delivery. SKIN-CAD also analyzes the
effects of metabolism and binding in the skin, dermal blood uptake,
iontophoresis, and so on.http://www.fqs.pl/chemistry_materials_life_science/products/skin_cad

SWizard is a user-friendly program (OS: MS Windows NT/2000/XP) for
postprocessing spectral data. A spectrum is calculated as a sum of Gaussian
or/and Lorentzian bands or the mixture of these functions please check http://www.sg-chem.net/swizard/

Swiss PDF viewer--an application that provides a user friendly interface
allowing to analyze several proteins at the same time
-- http://www.expasy.org/spdbv/

VLifeMDS (www.vlifesciences.com ) (VLife Molecule
Design Suite)
is an integrated platform for Computer Aided Drug Design (CADD) and molecule
discovery available for both Windows® and Linux platforms.
This integrated
suite provides complete toolkit to scientists to perform all scientific
functions required to pursue structure based as well as ligand based
discovery approaches.

ZMM Software, Inc. -- http://www.zmmsoft.com -- Molecular Modeling and
Simulation Software (MVM viewer is a freeware, ZMM is a molecular
modeling and simulation system that runs on Windows and Unix/Linux).

Disclaimer: The list is provided as a service to
the CCL community. However, no guarantees are given as to the suitability
or accuracy of this list. The text and the links to web sites were often
provided by vendors or taken from other web sites. Some of the information
may already be obsolete, since the list is not aggresively maintained
or reviewed. Please provide additions or correction to this list by
contacting the CCL.NET manager:
Jan Labanowski.
Email: jkl at ccl dot net.